MS-Mapper is a Java application, designed to create 2D-heatmaps of mass spectrometry data.
The current version just understands MZXML data, so you might need to convert your proprietary file formats first. You can choose between different color maps, e.g. heat colors or a gray scale. It also supports various scaling: logarithmic scale, scale by square root and no scaling at all. In addition the figure can be surrounded by a legend. At the moment only images in PNG format are supported, if you are interested in different image formats feel free to file a feature request. Image dimensions are determined by the user. A resulting image with heat colors, a logarithm scale and surrounded legends is displayed in figure 1.
The graphical user interface should be easy to understand, a screen-shot is attached in figure 2. If you anyway need help feel free to ping me. All you need to run it is a Java runtime environment, you can get one for free from java.com.